Endogenous retrovirus loci and induced changes in gene expression in Japanese indigenous chickens
Abstract When retroviruses infect germ cells and are transmitted to offspring, they become endogenous retroviruses (ERVs), whose insertions may influence the expression of nearby genes. In this study, we aimed to identify the genomic loci of ERVs in commercial broiler (Ross308), Tosa-Jidori, and Yak...
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Nature Portfolio
2025-04-01
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| author | Shinya Ishihara Jun-ichi Shiraishi Saki Shimamoto Daichi Ijiri |
| author_facet | Shinya Ishihara Jun-ichi Shiraishi Saki Shimamoto Daichi Ijiri |
| author_sort | Shinya Ishihara |
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| description | Abstract When retroviruses infect germ cells and are transmitted to offspring, they become endogenous retroviruses (ERVs), whose insertions may influence the expression of nearby genes. In this study, we aimed to identify the genomic loci of ERVs in commercial broiler (Ross308), Tosa-Jidori, and Yakido chickens, as well as to elucidate their impact on neighboring gene expression. Whole-genome data were obtained using next-generation sequencing, and candidate ERV loci were identified using the RetroSeq software. The Integrative Genomics Viewer tool was used to confirm target site duplications (TSDs) as evidence of ERV insertions. All reads within 200 bp of these TSDs were extracted to create contigs, confirming the presence of ERV sequences in the contigs using BLASTN. Gene expression levels were estimated by focusing on genes located near the 172 identified ERV loci. Among these, 119 loci were detected in broiler chickens, 80 in Tosa-Jidori chickens, and 86 in Yakido chickens, with 28 loci shared among them. Moreover, of these 172 loci, 75 were located within or near genes. Significant differences in gene expression were observed for N-acetylated alpha-linked acidic dipeptidase 2 (NAALAD2) and phosphoribosylaminoimidazolesuccinocarboxamide synthase (PAICS) depending on the presence of ERV insertions. These results suggest that ERV insertions may influence the expression of NAALAD2 and PAICS, providing insights into the genetic diversity and evolutionary background of commercial and indigenous chickens. Understanding the effects of ERV insertions on gene expression can inform future genetic research and poultry breeding programs aimed at improving health and productivity. |
| format | Article |
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| spelling | doaj-art-7a68da51df854614b516a7d7cdd0b56c2025-08-20T02:12:06ZengNature PortfolioScientific Reports2045-23222025-04-011511910.1038/s41598-025-96881-zEndogenous retrovirus loci and induced changes in gene expression in Japanese indigenous chickensShinya Ishihara0Jun-ichi Shiraishi1Saki Shimamoto2Daichi Ijiri3Department of Animal Science, Nippon Veterinary and Life Science UniversityDepartment of Animal Science, Nippon Veterinary and Life Science UniversityDepartment of Animal Science and Welfare, Joint Faculty of Veterinary Medicine, Kagoshima UniversityDepartment of Animal Science and Welfare, Joint Faculty of Veterinary Medicine, Kagoshima UniversityAbstract When retroviruses infect germ cells and are transmitted to offspring, they become endogenous retroviruses (ERVs), whose insertions may influence the expression of nearby genes. In this study, we aimed to identify the genomic loci of ERVs in commercial broiler (Ross308), Tosa-Jidori, and Yakido chickens, as well as to elucidate their impact on neighboring gene expression. Whole-genome data were obtained using next-generation sequencing, and candidate ERV loci were identified using the RetroSeq software. The Integrative Genomics Viewer tool was used to confirm target site duplications (TSDs) as evidence of ERV insertions. All reads within 200 bp of these TSDs were extracted to create contigs, confirming the presence of ERV sequences in the contigs using BLASTN. Gene expression levels were estimated by focusing on genes located near the 172 identified ERV loci. Among these, 119 loci were detected in broiler chickens, 80 in Tosa-Jidori chickens, and 86 in Yakido chickens, with 28 loci shared among them. Moreover, of these 172 loci, 75 were located within or near genes. Significant differences in gene expression were observed for N-acetylated alpha-linked acidic dipeptidase 2 (NAALAD2) and phosphoribosylaminoimidazolesuccinocarboxamide synthase (PAICS) depending on the presence of ERV insertions. These results suggest that ERV insertions may influence the expression of NAALAD2 and PAICS, providing insights into the genetic diversity and evolutionary background of commercial and indigenous chickens. Understanding the effects of ERV insertions on gene expression can inform future genetic research and poultry breeding programs aimed at improving health and productivity.https://doi.org/10.1038/s41598-025-96881-zEndogenous retrovirusJapanese Indigenous chickensWhole-genome sequencing |
| spellingShingle | Shinya Ishihara Jun-ichi Shiraishi Saki Shimamoto Daichi Ijiri Endogenous retrovirus loci and induced changes in gene expression in Japanese indigenous chickens Scientific Reports Endogenous retrovirus Japanese Indigenous chickens Whole-genome sequencing |
| title | Endogenous retrovirus loci and induced changes in gene expression in Japanese indigenous chickens |
| title_full | Endogenous retrovirus loci and induced changes in gene expression in Japanese indigenous chickens |
| title_fullStr | Endogenous retrovirus loci and induced changes in gene expression in Japanese indigenous chickens |
| title_full_unstemmed | Endogenous retrovirus loci and induced changes in gene expression in Japanese indigenous chickens |
| title_short | Endogenous retrovirus loci and induced changes in gene expression in Japanese indigenous chickens |
| title_sort | endogenous retrovirus loci and induced changes in gene expression in japanese indigenous chickens |
| topic | Endogenous retrovirus Japanese Indigenous chickens Whole-genome sequencing |
| url | https://doi.org/10.1038/s41598-025-96881-z |
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